--- /dev/null
+#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__
+#define __VIENNA_RNA_PACKAGE_COFOLD_H__
+
+#include "data_structures.h"
+
+#ifdef __GNUC__
+#define DEPRECATED(func) func __attribute__ ((deprecated))
+#else
+#define DEPRECATED(func) func
+#endif
+
+/**
+ * \addtogroup cofold
+ * \brief Predict structures formed by two molecules upon hybridization.
+ *
+ * The function of an RNA molecule often depends on its interaction with
+ * other RNAs. The following routines therefore allow to predict structures
+ * formed by two RNA molecules upon hybridization.\n
+ * One approach to co-folding two RNAs consists of concatenating the two
+ * sequences and keeping track of the concatenation point in all energy
+ * evaluations. Correspondingly, many of the cofold() and
+ * co_pf_fold() routines below take one sequence string as argument
+ * and use the the global variable #cut_point to mark the concatenation
+ * point. Note that while the <i>RNAcofold</i> program uses the '&' character
+ * to mark the chain break in its input, you should not use an '&' when using
+ * the library routines (set #cut_point instead).\n
+ * In a second approach to co-folding two RNAs, cofolding is seen as a
+ * stepwise process. In the first step the probability of an unpaired region
+ * is calculated and in a second step this probability of an unpaired region
+ * is multiplied with the probability of an interaction between the two RNAs.
+ * This approach is implemented for the interaction between a long
+ * target sequence and a short ligand RNA. Function pf_unstru() calculates
+ * the partition function over all unpaired regions in the input
+ * sequence. Function pf_interact(), which calculates the
+ * partition function over all possible interactions between two
+ * sequences, needs both sequence as separate strings as input.
+ *
+ */
+
+/**
+ * \addtogroup mfe_cofold
+ * @{
+ * \file cofold.h
+ *
+ * \brief MFE version of cofolding routines
+ *
+ * This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to
+ * MFE Cofolding...
+ * This also includes the Zuker suboptimals calculations, since they are implemented using the cofold
+ * routines.
+ */
+
+/**
+ * \brief Compute the minimum free energy of two interacting RNA molecules
+ *
+ * The code is analog to the fold() function. If #cut_point ==-1 results
+ * should be the same as with fold().
+ *
+ * \ingroup mfe_cofold
+ *
+ * \param sequence The two sequences concatenated
+ * \param structure Will hold the barcket dot structure of the dimer molecule
+ * \return minimum free energy of the structure
+ */
+float cofold( const char *sequence,
+ char *structure);
+
+/**
+ * \brief Compute the minimum free energy of two interacting RNA molecules
+ *
+ */
+float cofold_par( const char *string,
+ char *structure,
+ paramT *parameters,
+ int is_constrained);
+
+/**
+ * \brief Free memory occupied by cofold()
+ */
+void free_co_arrays(void);
+
+/**
+ * \brief Recalculate parameters
+ */
+void update_cofold_params(void);
+
+void update_cofold_params_par(paramT *parameters);
+
+
+/**
+ * \brief Export the arrays of partition function cofold (with gquadruplex support)
+ *
+ * Export the cofold arrays for use e.g. in the concentration
+ * Computations or suboptimal secondary structure backtracking
+ *
+ * \param f5_p A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
+ * \param c_p A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
+ * \param fML_p A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
+ * \param fM1_p A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
+ * \param fc_p A pointer to the 'fc' array, i.e. array ...
+ * \param ggg_p A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j]
+ * \param indx_p A pointer to the indexing array used for accessing the energy matrices
+ * \param ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j)
+ */
+void export_cofold_arrays_gq( int **f5_p,
+ int **c_p,
+ int **fML_p,
+ int **fM1_p,
+ int **fc_p,
+ int **ggg_p,
+ int **indx_p,
+ char **ptype_p);
+
+/**
+ * \brief Export the arrays of partition function cofold
+ *
+ * Export the cofold arrays for use e.g. in the concentration
+ * Computations or suboptimal secondary structure backtracking
+ *
+ * \param f5_p A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]
+ * \param c_p A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j
+ * \param fML_p A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem
+ * \param fM1_p A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem
+ * \param fc_p A pointer to the 'fc' array, i.e. array ...
+ * \param indx_p A pointer to the indexing array used for accessing the energy matrices
+ * \param ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j)
+ */
+void export_cofold_arrays(int **f5_p,
+ int **c_p,
+ int **fML_p,
+ int **fM1_p,
+ int **fc_p,
+ int **indx_p,
+ char **ptype_p);
+
+
+/**
+ * @}
+ */
+
+/**
+ * \brief Compute Zuker type suboptimal structures
+ *
+ * Compute Suboptimal structures according to M. Zuker, i.e. for every
+ * possible base pair the minimum energy structure containing the resp. base pair.
+ * Returns a list of these structures and their energies.
+ *
+ * \ingroup subopt_zuker
+ *
+ * \param string RNA sequence
+ * \return List of zuker suboptimal structures
+ */
+SOLUTION *zukersubopt(const char *string);
+
+/**
+ * \brief Compute Zuker type suboptimal structures
+ *
+ * \ingroup subopt_zuker
+ *
+ */
+SOLUTION *zukersubopt_par( const char *string,
+ paramT *parameters);
+
+/**
+ * \brief get_monomer_free_energies
+ *
+ * Export monomer free energies out of cofold arrays
+ *
+ * \param e1 A pointer to a variable where the energy of molecule A will be written to
+ * \param e2 A pointer to a variable where the energy of molecule B will be written to
+ */
+void get_monomere_mfes( float *e1,
+ float *e2);
+
+
+/**
+ * allocate arrays for folding
+ * \deprecated{This function is obsolete and will be removed soon!}
+ */
+DEPRECATED(void initialize_cofold(int length));
+
+#endif
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